I hope you can help me. I am attempting a
rna-seq analysis. This is a BAM file (the first ~100 lines are like above and the remaining lines are in this context with QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS SEQ QUAL OPT). I have the entire workflow done except for this part. I want to go from the raw data I was given to fastqsanger.gz so I can use trimmomatic on it, etc.
How do I go about that? Or another question, what am I doing wrong?
These tutorials cover many common analysis paths when working with RNA-seq data. Start with a few introduction tutorials if you are not familiar with Galaxy, then review tutorials that match the type of analysis you want to do. Both will help you to understand what to do when using your own data.
BAM datasets are intermediate output. These represent alignments of read sequences against a reference sequence. Mapping tools generate this kind of data.
The raw RNA-seq read sequencing data should already be in “fastqsanger” format, or “fastqsanger.gz” if compressed. When uploading this kind of data (fastq) to Galaxy, leave the datatype detection as “auto-detect”. If the data really is in this format, Galaxy will guess it correctly and QA tools like Trimmomatic will accept it as valid input.
If you need more help, please be specific when you ask a new question so we can help you. What are the analysis goals? What steps have you done so far? If you ran into job errors: what did you check already, what did the error logs report, and can you share a link to your work for context?